feat: Enhance MCP server capabilities and improve root management

[modesty]

• Implemented support for Root capability to replace the cwd in session, including handling roots/list requests and notifications for root changes.
• Updated package version to 0.0.12.
• Added requestRootsFromClient method to handle root requests from the client and manage responses.
• Improved logging for root updates and added validation for root URIs.
• Enhanced ToolsManager to avoid duplicate root updates and log details about the update process.
• Updated CLI command tools to only log changes when roots are actually updated.
• Refactored tests to cover new root management features and ensure proper handling of notifications and requests.
• Improved error handling for invalid response formats when requesting roots.